Société Française de Bioinformatique

Mots-Clés

eQTL transcriptomique génomique Neuroinflammation NMOSD MOGAD

Description

Title: Identification of expressed Quantitative Trait Loci (eQTL) by integrating genomic and transcriptomic data in NMOSD disease
Context:
Neuromyelitis optica spectrum disorder (NMOSD) is a rare neuroinflammatory disease with unclear etiology. NMSOD is characterised (but not strictly limited to) by the presence of aquaporin-4 immunoglobulin G autoantibodies (AQP4-IgG), which target the water channel protein aquaporin-4 in the central nervous system. Some key clinical symptoms of NMOSD are visual defect/loss caused by optic neuritis, myelitis in the cervical and upper spinal cord, and many other brainstem syndrome symptoms.
In our project, multi-layer of omics analysis was performed to have a comprehensive view of the molecular architecture of the disease. By integrating genotype and transcriptomic data, we will assess the regulatory effects of disease-associated variants on gene expression and identify the genes potentially affected by these variants. Currently, there is no NMOSD disease-specific eQTL database, which limits our ability to characterise disease-relevant regulatory effects. Therefore, the establishment of an NMOSD-specific eQTL database is essential to provide a dedicated resource for investigating the functional consequences of disease-associated genetic variants and their potential effects on gene expression.
Objective:
The main objective of the internship is to build NMOSD-specific eQTLs database using GWAS data and mRNA data.
Resource:
The GWAS data and mRNA data on matching patients are already available.
All the scripts and pipeline are also available
Missions:
- eQTL mapping with linear regression
- Co-localisation
- Maintain and update the analysis code in Git
- Interpret biological results
Skills:
- Expected:
• Proficiency in Python and R
• Good knowledge of statistics
• Good level in English (written and spoken)
• Interest in immunology/neuroinflamantory disease
- Appreciated :
• High-performance computing
• Git
• PLINK/BCFtools, tensorQTL
- Working language : English